LAMMPS (27 Nov 2018)
  using 1 OpenMP thread(s) per MPI task
# 2d indenter simulation

dimension	2
boundary	p s p

atom_style	atomic
neighbor	0.3 bin
neigh_modify	delay 5

# create geometry

lattice		hex 0.9
Lattice spacing in x,y,z = 1.1327 1.96189 1.1327
region		box block 0 20 0 10 -0.25 0.25
create_box	2 box
Created orthogonal box = (0 0 -0.283174) to (22.6539 19.6189 0.283174)
  1 by 1 by 1 MPI processor grid
create_atoms	1 box
Created 420 atoms
  Time spent = 0.000351191 secs

mass		1 1.0
mass		2 1.0

# LJ potentials

pair_style	lj/cut 2.5
pair_coeff	* * 1.0 1.0 2.5

# define groups

region	        1 block INF INF INF 1.25 INF INF
group		lower region 1
60 atoms in group lower
group		mobile subtract all lower
360 atoms in group mobile
set		group lower type 2
  60 settings made for type

# initial velocities

compute	  	new mobile temp
velocity	mobile create 0.2 482748 temp new
fix		1 all nve
fix		2 lower setforce 0.0 0.0 0.0
fix		3 all temp/rescale 100 0.1 0.1 0.01 1.0

# run with indenter

timestep	0.003
variable	k equal 1000.0/xlat
variable        y equal "13.0*ylat - step*dt*0.02*ylat"

fix		4 all indent $k sphere 10 v_y 0 5.0
fix		4 all indent 882.849286914813 sphere 10 v_y 0 5.0
fix		5 all enforce2d

thermo		1000
thermo_modify	temp new
WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:488)

#dump		1 all atom 250 dump.indent

#dump		2 all image 1000 image.*.jpg type type #		zoom 1.6 adiam 1.5
#dump_modify	2 pad 5

#dump		3 all movie 1000 movie.mpg type type #		zoom 1.6 adiam 1.5
#dump_modify	3 pad 5

run		30000
Neighbor list info ...
  update every 1 steps, delay 5 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 2.8
  ghost atom cutoff = 2.8
  binsize = 1.4, bins = 17 15 1
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair lj/cut, perpetual
      attributes: half, newton on
      pair build: half/bin/atomonly/newton
      stencil: half/bin/2d/newton
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.043 | 3.043 | 3.043 Mbytes
Step Temp E_pair E_mol TotEng Press Volume 
       0          0.2   -3.1727576            0   -3.0018052    -1.436185    444.53333 
    1000   0.11974254   -3.0876892            0   -2.9853378 -0.037059247    440.78771 
    2000   0.12086797   -3.0886512            0   -2.9853378  -0.39883289     444.3556 
    3000   0.11671309   -3.0840074            0   -2.9842455  -0.34859991    442.95428 
    4000   0.12339115   -3.1000529            0   -2.9945828 -0.049696765    438.99297 
    5000   0.10860594   -3.0866045            0   -2.9937722  -0.47973882    443.99855 
    6000   0.11839788   -3.0929689            0   -2.9917669 -0.033454196    442.70339 
    7000   0.12194527   -3.0835584            0   -2.9793242  -0.13981611    443.36261 
    8000   0.11671309   -3.0862884            0   -2.9865265  0.073952568    441.71327 
    9000   0.12449823   -3.0880806            0   -2.9816643   0.28647997    439.28167 
   10000   0.12475263   -3.0830722            0   -2.9764384   0.38101457    440.50309 
   11000   0.11198118   -3.0743549            0   -2.9786377   0.67583952    438.50252 
   12000   0.10823034   -3.0621355            0   -2.9696244   0.66485023    441.13781 
   13000    0.1194298   -3.0579575            0   -2.9558734    1.0884087    437.72805 
   14000   0.12310404    -3.051382            0   -2.9461573   0.87077685    445.54012 
   15000   0.11148458   -3.0402208            0    -2.944928    1.0040641     451.9079 
   16000   0.12322323    -3.041552            0   -2.9362254    0.7581871    456.90367 
   17000   0.12311085   -3.0300334            0   -2.9248029    1.0483261    452.91646 
   18000   0.12062509   -3.0261636            0   -2.9230579    1.3983564    451.71896 
   19000   0.11957854   -3.0142948            0   -2.9120836    1.3961883    457.92501 
   20000   0.12230825   -3.0015681            0   -2.8970237    1.1238267    470.13177 
   21000    0.1206722   -3.0280371            0   -2.9248911   0.77173089    472.88673 
   22000   0.11522969   -3.0159631            0   -2.9174691   0.58945089    474.56136 
   23000    0.1169292   -3.0257398            0   -2.9257932   0.90016236    473.58055 
   24000   0.11814748   -3.0288882            0   -2.9279002   0.85469502    469.82134 
   25000   0.11141357   -3.0218783            0   -2.9266463    1.0469177    471.01085 
   26000   0.11159246   -3.0122701            0   -2.9168851    1.1216321    471.99194 
   27000   0.10918089   -3.0045635            0   -2.9112398    1.2920286    474.41152 
   28000    0.1183178   -3.0017823            0   -2.9006488    1.3477212    474.08453 
   29000     0.118332   -2.9855957            0     -2.88445    1.4002777    478.49231 
   30000   0.11691453   -2.9721091            0    -2.872175    1.6266108     479.0394 
Loop time of 2.58797 on 1 procs for 30000 steps with 420 atoms

Performance: 3004676.853 tau/day, 11592.117 timesteps/s
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 1.7803     | 1.7803     | 1.7803     |   0.0 | 68.79
Neigh   | 0.074505   | 0.074505   | 0.074505   |   0.0 |  2.88
Comm    | 0.038266   | 0.038266   | 0.038266   |   0.0 |  1.48
Output  | 0.00033927 | 0.00033927 | 0.00033927 |   0.0 |  0.01
Modify  | 0.61562    | 0.61562    | 0.61562    |   0.0 | 23.79
Other   |            | 0.07897    |            |       |  3.05

Nlocal:    420 ave 420 max 420 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:    111 ave 111 max 111 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:    3711 ave 3711 max 3711 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 3711
Ave neighs/atom = 8.83571
Neighbor list builds = 614
Dangerous builds = 0

# run without indenter

unfix           4
run		30000
Per MPI rank memory allocation (min/avg/max) = 3.043 | 3.043 | 3.043 Mbytes
Step Temp E_pair E_mol TotEng Press Volume 
   30000   0.11691453   -2.9721091            0    -2.872175    1.6267079     479.0108 
   31000   0.10925212   -3.0270482            0   -2.9336637  -0.33277278    488.93429 
   32000   0.11439597   -2.9975157            0   -2.8997344  -0.41937391    489.30458 
   33000    0.1202415   -3.0272086            0   -2.9244307   0.45435486    481.29876 
   34000   0.12236916   -3.0291826            0   -2.9245861  0.060773047    480.57112 
   35000   0.10701052   -3.0155083            0   -2.9240398  -0.32828426    491.34913 
   36000   0.11671309   -3.0501978            0   -2.9504359   0.17774604    480.03548 
   37000   0.11311041   -3.0472325            0   -2.9505501 -0.096250401    480.52043 
   38000   0.11671309   -3.0386964            0   -2.9389345  -0.26914235     481.1656 
   39000     0.127378   -3.0478959            0   -2.9390181  -0.11503417    478.38488 
   40000   0.11422635   -3.0479185            0   -2.9502821  -0.11840551    479.29223 
   41000   0.11339443   -3.0470107            0   -2.9500855  -0.36658233    484.33262 
   42000   0.11750945   -3.0506884            0   -2.9502458  -0.18687218    482.18706 
   43000   0.10968886   -3.0433967            0   -2.9496388  -0.23827778    483.87888 
   44000   0.11163929   -3.0449886            0   -2.9495636   -0.2241347    482.09898 
   45000   0.11726053   -3.0498339            0   -2.9496041  -0.03707734    480.27988 
   46000   0.10971187   -3.0434544            0   -2.9496769    -0.311219    482.26813 
   47000   0.11448154   -3.0476146            0   -2.9497602  -0.10374643    480.75372 
   48000   0.11796515   -3.0503583            0   -2.9495262  -0.18534074    479.03433 
   49000   0.11331324   -3.0464609            0   -2.9496051  -0.38382421    483.23363 
   50000    0.1102072    -3.043921            0     -2.94972  -0.11678189    481.28121 
   51000   0.11169997   -3.0449271            0   -2.9494503  -0.22869529    483.39421 
   52000    0.1052379   -3.0396306            0   -2.9496773    -0.264831    479.77275 
   53000   0.12170796   -3.0536766            0   -2.9496453  -0.14056206    482.58519 
   54000   0.11347849   -3.0465613            0   -2.9495642  -0.23137478       481.27 
   55000     0.115223   -3.0480538            0   -2.9495655  -0.32336031    485.15401 
   56000   0.11115417    -3.044689            0   -2.9496787 -0.066353134    481.37281 
   57000   0.10783414   -3.0418895            0    -2.949717  -0.20380917    482.14483 
   58000   0.10703451     -3.04105            0    -2.949561   -0.2673909    482.03847 
   59000   0.11041464   -3.0439806            0   -2.9496023  -0.17616699    481.33957 
   60000   0.12014097     -3.05226            0    -2.949568  -0.21176633    481.15213 
Loop time of 2.20628 on 1 procs for 30000 steps with 420 atoms

Performance: 3524485.426 tau/day, 13597.552 timesteps/s
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 1.7599     | 1.7599     | 1.7599     |   0.0 | 79.77
Neigh   | 0.074152   | 0.074152   | 0.074152   |   0.0 |  3.36
Comm    | 0.037216   | 0.037216   | 0.037216   |   0.0 |  1.69
Output  | 0.00033259 | 0.00033259 | 0.00033259 |   0.0 |  0.02
Modify  | 0.25688    | 0.25688    | 0.25688    |   0.0 | 11.64
Other   |            | 0.07779    |            |       |  3.53

Nlocal:    420 ave 420 max 420 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:    106 ave 106 max 106 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:    3578 ave 3578 max 3578 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 3578
Ave neighs/atom = 8.51905
Neighbor list builds = 617
Dangerous builds = 0
Total wall time: 0:00:04
